Modify epub will write the current metadata to the metadata fields within the EPUB file, which is not what you want at all.
What you want is to change the actual filenames, as in
Code:
C:\\Users\<username>\Calibre Library\Joe Author\My Book (1)\My Book - Joe Author.epub
calibre will
automatically name the file according to the metadata
in the library view.
The filename will be according to
Code:
{location of library}\{authors}\{title} {id}\{title} - {authors}.{format}
If the title field
in calibre says "Mahouka Koukou no Rettousei - Volum (some random number)" then that is what will be filled in for {title} and that is how calibre will save it in the library folder.
There is no way to tell calibre to arbitrarily change the filename of the book. You must make sure the title and author fields in calibre are exactly what they should be.
calibre does not care what filenames you used to have for the book. It does not use that metatdata unless you go to Preferences ==> Import/Export ==> Adding books, in the tab "The Add Process", and uncheck the option "read metadata from file contents rather than file name".